Updated mtCOI reference dataset for the Bemisia tabaci species complex

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Boykin" }, { "@type": "Person", "name": "Anders Savill" }, { "@type": "Person", "name": "Paul De Barro" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": "Members of the whitefly Bemisia tabaci species complex cause millions of dollars of damage globally and are considered one of the world’s most invasive species. They are capable of causing extensive damage to major vegetable, grain legume and fiber crops. All member of the species complex are morphologically identical therefore, data from the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequence has been used to identify the various species. The current reference dataset that is widely used is found on the CSIRO data portal. However, the reference set stored on the CSIRO data does not include newly added sequences (2013-2017), therefore an updated reference dataset is needed. All mtCOI data for the Bemisia tabaci species complex were downloaded on 22 May 2017 from GenBank and after quality checking, a dataset of 1,071 unique sequences and 696 base pairs was generated (https://doi.org/10.6084/m9.figshare.5437420.v1)." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/6-1835", "name": "Updated mtCOI reference dataset for the Bemisia tabaci species complex" } } ] } Home Browse Updated mtCOI reference dataset for the Bemisia tabaci species complex ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Boykin LM, Savill A and De Barro P. Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.12688/f1000research.12858.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Data Note Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] Laura M. Boykin https://orcid.org/0000-0002-6101-1921 1 , Anders Savill 1 , Paul De Barro 2 Laura M. Boykin https://orcid.org/0000-0002-6101-1921 1 , Anders Savill 1 , Paul De Barro 2 PUBLISHED 13 Oct 2017 Author details Author details 1 School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA, Australia 2 CSIRO, Ecosciences Precinct, Brisbane, QLD, Australia Laura M. Boykin Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Anders Savill Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Paul De Barro Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Agriculture, Food and Nutrition gateway. Abstract Members of the whitefly Bemisia tabaci species complex cause millions of dollars of damage globally and are considered one of the world’s most invasive species. They are capable of causing extensive damage to major vegetable, grain legume and fiber crops. All member of the species complex are morphologically identical therefore, data from the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequence has been used to identify the various species. The current reference dataset that is widely used is found on the CSIRO data portal. However, the reference set stored on the CSIRO data does not include newly added sequences (2013-2017), therefore an updated reference dataset is needed. All mtCOI data for the Bemisia tabaci species complex were downloaded on 22 May 2017 from GenBank and after quality checking, a dataset of 1,071 unique sequences and 696 base pairs was generated (https://doi.org/10.6084/m9.figshare.5437420.v1). READ ALL READ LESS Keywords species identification, whitefly, insect vector, mitochondrial cytochrome oxidase, DNA barcoding Corresponding Author(s) Laura M. Boykin ( [email protected] ) Close Corresponding author: Laura M. Boykin Competing interests: The authors have no competing interests. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2017 Boykin LM et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Boykin LM, Savill A and De Barro P. Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.12688/f1000research.12858.1 ) First published: 13 Oct 2017, 6 :1835 ( https://doi.org/10.12688/f1000research.12858.1 ) Latest published: 13 Oct 2017, 6 :1835 ( https://doi.org/10.12688/f1000research.12858.1 ) Introduction Members of the Bemisia tabaci (whiteflies) species complex are among the world’s most devastating insect pests and cause billions of dollars (US) of damage each year, leaving farmers in the developing world food insecure ( De Barro et al. , 2011 ). As a species complex with at least 34 members, identification is based on the use of the 657 bp portion of the 3’ end of the mitochondrial COI (mtCOI) ( Boykin et al ., 2012 , Boykin et al ., 2013 ). In order to identify members of the complex correctly, a curated reference dataset is a useful resource. In 2012, a reference mtCOI dataset was made available on the CSIRO data portal ( De Barro & Boykin, 2012 ). Errors in the dataset were subsequently identified and so the dataset was updated on 15 May 2017 ( http://doi.org/10.4225/08/591a4018dfca8 ) ( De Barro & Boykin, 2017 ), but did not include new additions from GenBank (post 2012). Therefore, the dataset described herein represents the most up-to-date reference resource for members of the complex. Methods The CSIRO dataset ( http://doi.org/10.4225/08/591a4018dfca8 ), updated 15 May 2017 was used as the starting point. The existing records were updated to include host plant data. New records post-2012 were then downloaded on 22 May 2017 directly from GenBank. All downloaded data was treated as follows: 1) Data was classified with BLAST using the new CSIRO reference data set 2) Sequences that caused gaps in the alignment were removed 2) Sequences that had stop codons present were removed 3) Clustal Omega ( Sievers & Higgins, 2014 ) was used for preliminary alignment and fine tuning of the alignment was carried out with MAFFT ( Katoh & Standley, 2013 ). 4) Duplicate sequences were then removed using BBMAP Dedupe ( Bushnell, 2017 ). In addition, all MEAM2 sequences were removed as they have now been confirmed to be pseudogenes ( Tay et al ., 2017 ). Data availability Figshare: Dataset 1. mtCOI reference data for species ID of Bemisia tabaci . DOI: 10.6084/m9.figshare.5437420 ( Boykin et al ., 2017 ) Competing interests The authors have no competing interests. Grant information The author(s) declared that no grants were involved in supporting this work. F1000 recommended References Boykin LM, Armstrong KF, Kubatko L, et al. : Species delimitation and global biosecurity. Evol Bioinform Online. 2012; 8 : 1–37. PubMed Abstract | Publisher Full Text | Free Full Text Boykin LM, Bell CD, Evans G, et al. : Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed. BMC Evol Biol. 2013; 13 : 228. PubMed Abstract | Publisher Full Text | Free Full Text Boykin L, Savill A, De Barro P: mtCOI reference data for species ID of Bemisia tabaci . figshare. 2017. Data Source Bushnell B: BBmap. 2017. Reference Source De Barro P, Boykin LM: Global Bemisia dataset release version 31 Dec 2012. CSIRO. 2012. Publisher Full Text De Barro P, Boykin LM: Global Bemisia dataset release version 15 May 2017. CSIRO. 2017. Publisher Full Text De Barro PJ, Liu SS, Boykin LM, et al. : Bemisia tabaci : a statement of species status. Annu Rev Entomol. 2011; 56 : 1–19. PubMed Abstract | Publisher Full Text Katoh K, Standley DM: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30 (4): 772–780. PubMed Abstract | Publisher Full Text | Free Full Text Sievers F, Higgins DG: Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol. 2014; 1079 : 105–116. PubMed Abstract | Publisher Full Text Tay WT, Elfekih S, Court LN, et al. : The trouble with MEAM2: Implications of pseudogenes on species delimitation in the globally invasive Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex. Genome Biol Evol. 2017. PubMed Abstract | Publisher Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 13 Oct 2017 ADD YOUR COMMENT Comment Author details Author details 1 School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA, Australia 2 CSIRO, Ecosciences Precinct, Brisbane, QLD, Australia Laura M. Boykin Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Anders Savill Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Paul De Barro Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Competing interests The authors have no competing interests. Grant information The author(s) declared that no grants were involved in supporting this work. Article Versions (1) version 1 Published: 13 Oct 2017, 6:1835 https://doi.org/10.12688/f1000research.12858.1 Copyright © 2017 Boykin LM et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Boykin LM, Savill A and De Barro P. Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.12688/f1000research.12858.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 13 Oct 2017 Views 0 Cite How to cite this report: Saurabh S and Mishra M. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26987 ) The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26987 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 08 Nov 2017 Sharad Saurabh , Molecular and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India Manisha Mishra , Developmental Toxicology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India Approved VIEWS 0 https://doi.org/10.5256/f1000research.13935.r26987 Whitefly ( Bemisia tabaci ) is becoming a global hazard for crop and ornamental plants. Identification of correct species is always better for the implication of best control strategy. In this regard, the effort made by Boykin et al for speedy and ... Continue reading READ ALL Whitefly ( Bemisia tabaci ) is becoming a global hazard for crop and ornamental plants. Identification of correct species is always better for the implication of best control strategy. In this regard, the effort made by Boykin et al for speedy and accurate identification of B. tabaci species complex is very significant. Additionally, the dataset developed with enriched quality is also very useful for whitefly biologist working in the area of evolution, mitochondrial genomics and crop management. All the bioinformatics tools used to generate this refined dataset are ideal to make such analysis. Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests: No competing interests were disclosed. We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Saurabh S and Mishra M. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26987 ) The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26987 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Sakate RK. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26988 ) The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26988 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 23 Oct 2017 Renate Krause Sakate , Department of Plant Protection, Faculty of Agronomic Sciences, São Paulo State University (UNESP), Botucatu, Brazil Approved VIEWS 0 https://doi.org/10.5256/f1000research.13935.r26988 The updated mtCOI reference dataset for the Bemisia tabaci species complex will add a valuable contribution to researches for a fast and accurate identification of members from the B. tabaci species complex based on the partial mitochondrial COI gene. ... Continue reading READ ALL The updated mtCOI reference dataset for the Bemisia tabaci species complex will add a valuable contribution to researches for a fast and accurate identification of members from the B. tabaci species complex based on the partial mitochondrial COI gene. The high quality data is easily accessible for download and gathers whiteflies collected globally. The availability of a reliable and updated reference dataset is an essential tool that will aid the scientific community to identify and classify correctly this pest, the first step in the crop management against whiteflies. Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests: No competing interests were disclosed. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Sakate RK. Reviewer Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26988 ) The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26988 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 13 Oct 2017 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 Version 1 13 Oct 17 read read Renate Krause Sakate , São Paulo State University (UNESP), Botucatu, Brazil Sharad Saurabh , CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India Manisha Mishra , CSIR-Indian Institute of Toxicology Research, Lucknow, India Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2017 Saurabh S et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 08 Nov 2017 | for Version 1 Sharad Saurabh , Molecular and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India Manisha Mishra , Developmental Toxicology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India 0 Views copyright © 2017 Saurabh S et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Whitefly ( Bemisia tabaci ) is becoming a global hazard for crop and ornamental plants. Identification of correct species is always better for the implication of best control strategy. In this regard, the effort made by Boykin et al for speedy and accurate identification of B. tabaci species complex is very significant. Additionally, the dataset developed with enriched quality is also very useful for whitefly biologist working in the area of evolution, mitochondrial genomics and crop management. All the bioinformatics tools used to generate this refined dataset are ideal to make such analysis. Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests No competing interests were disclosed. We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Saurabh S and Mishra M. Peer Review Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26987) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26987 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2017 Sakate R. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 23 Oct 2017 | for Version 1 Renate Krause Sakate , Department of Plant Protection, Faculty of Agronomic Sciences, São Paulo State University (UNESP), Botucatu, Brazil 0 Views copyright © 2017 Sakate R. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions The updated mtCOI reference dataset for the Bemisia tabaci species complex will add a valuable contribution to researches for a fast and accurate identification of members from the B. tabaci species complex based on the partial mitochondrial COI gene. The high quality data is easily accessible for download and gathers whiteflies collected globally. The availability of a reliable and updated reference dataset is an essential tool that will aid the scientific community to identify and classify correctly this pest, the first step in the crop management against whiteflies. Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests No competing interests were disclosed. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Sakate RK. Peer Review Report For: Updated mtCOI reference dataset for the Bemisia tabaci species complex [version 1; peer review: 2 approved] . F1000Research 2017, 6 :1835 ( https://doi.org/10.5256/f1000research.13935.r26988) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/6-1835/v1#referee-response-26988 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. 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